Variant report

Variant	rs1472357
Chromosome Location	chr5:167615217-167615218
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EP300	chr5:167613029-167615681	SK-N-SH	brain:	n/a	chr5:167614699-167614713
2	GATA2	chr5:167613559-167615442	SH-SY5Y	brain:	n/a	n/a
3	MXI1	chr5:167613440-167615693	SK-N-SH	brain:	n/a	n/a
4	NFYB	chr5:167615211-167615377	GM12878	blood:	n/a	n/a
5	RFX5	chr5:167614126-167615731	SK-N-SH	brain:	n/a	n/a

Variant related genes	Relation type
ENSG00000253925	TF binding region

Extended variants
information (count: 13 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11134491	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13161927	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1472356	1.00[ASW][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1874461	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1874462	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4246813	0.92[ASN][1000 genomes]
rs4976577	0.84[ASN][1000 genomes]
rs4976578	1.00[ASW][hapmap];0.81[CEU][hapmap];0.85[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4976580	0.81[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs62383456	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs62383457	0.94[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6879767	1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9313398	0.85[YRI][hapmap]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1472357	GABRP	cis	cerebellum	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:167592400-167626000	Weak transcription	HSMM	muscle
2	chr5:167603600-167617200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr5:167606400-167617200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr5:167606600-167626800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr5:167608400-167616200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr5:167608600-167631800	Weak transcription	NH-A	brain
7	chr5:167609600-167619000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr5:167613200-167615400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr5:167613200-167615400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr5:167613200-167615400	Strong transcription	NHEK	skin
11	chr5:167613200-167615800	Enhancers	Fetal Heart	heart
12	chr5:167613400-167615600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr5:167613400-167615600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr5:167613600-167615800	Enhancers	Brain Germinal Matrix	brain
15	chr5:167614000-167615800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr5:167614400-167620400	Weak transcription	HSMMtube	muscle
17	chr5:167614600-167618800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr5:167614600-167620400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr5:167614600-167620600	Weak transcription	Fetal Brain Female	brain
20	chr5:167614800-167617400	Weak transcription	Right Ventricle	heart
21	chr5:167614800-167620600	Weak transcription	Stomach Smooth Muscle	stomach
22	chr5:167615000-167615400	Weak transcription	Fetal Brain Male	brain
23	chr5:167615000-167617200	Weak transcription	Left Ventricle	heart

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